Background

Writing documents in R Markdown is relatively straightforward once you know some of the basics. You can create many different formats, including .pdf, .html, and .doc, and customize them in a variety of ways.

Templates

There are a number of existing templates available in the rticles package that you can use for knitting your document to a specific style in .pdf format. For .html formats, there are a variety of “themes” available as well. For example, this document was created with the readable theme.

Equations

You can write nicely formatted equations in R Markdown using LaTeX language constructs. Although the initial leap into LaTeX can be a bit daunting, it gets much easier with some practice and help from the many guides available online (eg, math and document).

Here are a few things to help you get started (with examples below):

  • The default typeface is italic, which is commonly used to indicate a scalar; vectors and matrices are typically denoted with bold face, but you’ll need special coding to indicate them as such;

  • Sub- and superscripts are denoted by _ and ^, respectively; any text/number longer than one character/digit must be enclosed in curly braces {}

Inline

You can include equations inline by enabling the “inline math mode” through the use of a single dollar sign ($) at the beginning and end of the equation. For example,

The errors are normally distributed, such that $e_{i,j} \sim \text{N}(0, \sigma^2)$.

will render as

“The errors are normally distributed, such that \(e_{i,j} \sim \text{N}(0, \sigma^2)\).”

Stand alone

In many cases, you may want to have your equations set apart from the text on lines by themselves. To do this in Markdown, begin and end the equation block with 2 dollar signs ($$). If you want equations on multiple lines, use \\ to indicate a line break. For example,

$$
y_{i,j} = \alpha + \beta x_{i,j} + e_{i,j} \\
e_{i,j} \sim \text{N}(0, \sigma^2)
$$

will render to

\[ y_{i,j} = \alpha + \beta x_{i,j} + e_{i,j} \\ e_{i,j} \sim \text{N}(0, \sigma^2) \]

and

$$
\mathbf{x}_t = \mathbf{B} \mathbf{x}_{t-1} + \mathbf{C} \mathbf{c}_t + \mathbf{w}_t \\
\mathbf{y}_t = \mathbf{Z} \mathbf{x}_t + \mathbf{a} + \mathbf{v}_t
$$

would give

\[ \mathbf{x}_t = \mathbf{B} \mathbf{x}_{t-1} + \mathbf{C} \mathbf{c}_t + \mathbf{w}_t \\ \mathbf{y}_t = \mathbf{Z} \mathbf{x}_t + \mathbf{a} + \mathbf{v}_t \]

You can also use some additional LaTeX options inside the equation block for additional formatting options. For example, the aligned command can be used with an ampersand & to align multiple equations, such that

\begin{aligned}
  y &= 2x + x^2 + 3 \\
    &= x(2 + x) + 3
\end{aligned}

yields

\[ \begin{aligned} y &= 2x + x^2 + 3 \\ &= x(2 + x) + 3 \end{aligned} \]

Multiline equations in pdf

It turns out that pandoc won’t properly render multiline equations in .pdf format when demarking them with double dollar signs ($$). Instead, you’ll need to use the LaTeX commands \begin{equation} and \end{equation} to set them apart. For example,

\begin{equation}
y_{i,j} = \alpha + \beta x_{i,j} + e_{i,j} \\
e_{i,j} \sim \text{N}(0, \sigma^2)
\begin{equation}

will render to

\[\begin{equation} y_{i,j} = \alpha + \beta x_{i,j} + e_{i,j} \\ e_{i,j} \sim \text{N}(0, \sigma^2) \end{equation}\]

It turns out that this format works with .html formats as well, so you may just want to get in the habit of using this form.

Tables

There are several ways to create tables in R Markdown documents, but they vary in format based on your chosen output format. For .html documents, you can create simple tables with pipes (|) and colons (:). For example,

| Tables        | Are           | Cool  |
| ------------- |:-------------:| -----:|
| col 3 is      | right-aligned | $1600 |
| col 2 is      | centered      |   $12 |
| col 1 is      | left-aligned  |    $1 |

will result in

Tables Are Cool
col 3 is right-aligned $1600
col 2 is centered $12
col 1 is left-aligned $1

Note that the above code has been formatted for easier reading, but you wouldn’t have to do that. For example,

| Tables | Are | Cool |
| --- |:---:| ---:|
| col 3 is | right-aligned | $1600 |
| col 2 is | centered | $12 |
| col 1 is | left-aligned | $1 |

will give the same result

Tables Are Cool
col 3 is right-aligned $1600
col 2 is centered $12
col 1 is left-aligned $1

{kableExtra}

You can create much fancier tables with the {kableExtra} package (click here for the vignette with lots of examples). For example, the following code will create a table with striped rows, custom column widths, and a scroll box.

## load package
library(kableExtra)

## create exanple data frame
tbl_txt <- palmerpenguins::penguins[1:20, c(1, 2, 8, 7, 6)]
colnames(tbl_txt) <- c("Species", "Island", "Year", "Sex", "Body mass")

## generate table
kable(tbl_txt, format = "html",
      caption = "Table 1. An example of a `kableExtra` table.",
      align = "ccccr", escape = FALSE) %>%
  kable_styling(bootstrap_options = "striped",
                full_width = FALSE,
                position = "left") %>%
  column_spec(c(1,3,4,5), width = "6em") %>%
  column_spec(2, width = "12em") %>%
  scroll_box(height = "300px", extra_css = "border-style: none;")
Table 1. An example of a kableExtra table.
Species Island Year Sex Body mass
Adelie Torgersen 2007 male 3750
Adelie Torgersen 2007 female 3800
Adelie Torgersen 2007 female 3250
Adelie Torgersen 2007 NA NA
Adelie Torgersen 2007 female 3450
Adelie Torgersen 2007 male 3650
Adelie Torgersen 2007 female 3625
Adelie Torgersen 2007 male 4675
Adelie Torgersen 2007 NA 3475
Adelie Torgersen 2007 NA 4250
Adelie Torgersen 2007 NA 3300
Adelie Torgersen 2007 NA 3700
Adelie Torgersen 2007 female 3200
Adelie Torgersen 2007 male 3800
Adelie Torgersen 2007 male 4400
Adelie Torgersen 2007 female 3700
Adelie Torgersen 2007 female 3450
Adelie Torgersen 2007 male 4500
Adelie Torgersen 2007 female 3325
Adelie Torgersen 2007 male 4200

Figures

Another of Markdown’s strengths is its ability to render high-quality figures. This can be done by either inserting links to saved figures/images as shown above, or executing R code to do so. For example, this code

```{r xy_plot}
set.seeed(123)
n <- 100
x <- runif(nn, 0, 10)
e <- rnorm(nn)
y <- 1 + 0.5 * x + e
plot(x, y)
```

would produce the following plot

You can also add chunk options to change the figure’s size, location, etc. For example,

```{r xy_plot, fig.height = 4, fig.width = 4, fig.align = "center"}
set.seed(497)
n <- 100
x <- runif(n, 0, 10)
e <- rnorm(n)
y <- 1 + 0.5 * x + e
plot(x, y)
```

would instead yield

References

R Markdown is set up to use BibTeX-style references and format the citations accordingly. To do so, you’ll need to have your references in a BibTeX library with a .bib extension.

Creating a .bib file

One option is to manually create reference entries, but there are several methods for exporting references from reference management software, such as EndNote or Zotero.

Export from Zotero

To export your citations from Zotero, do the following

  • Select the library you wish to export
  • From the menu, choose File > Export Library
  • On the next screen, choose BibTeX from the dropdown menu & click OK
  • Navigate to the directory where you want to save your file & save it with a .bib suffix

Export from EndNote

To export a reference library from EndNote, do the following

  • From the main menu, select Edit > Output Styles > Open Style Manager...

  • Enter “bibtex” into the search bar at the top of the pop-up window and check the box next to BibTeX Export

  • Close the window when you’re finished

  • From the main menu, select Edit > Output Styles and check the BibTeX Export option

  • From the main menu, select File > Export...

  • Make sure to give your filename a .bib suffix and verify that the options Text only and BibTeX Export are selected

  • Click Save when you’re finished

Export from Mendeley

To export a reference library from Mendeley, do the following

  • Go to the Mendeley Preferences menu

  • Click on the BibTeX tab

  • Check the box next to Enable BibTeX syncing

  • Click the radio button next to Create one BibTeX file per group

  • Change the Path to your desired location for the library files

  • Click OK when you are finished

Citations

YAML

The first step in getting properly formatted citations and references in R Markdown documents is to specify two pieces of information in the documents YAML:

  1. the name of of the .bib file containing the references

  2. the name of the style file that specifies how the references will be formatted in the printed docuement.

So, for example, the information for this document is

bibliography: "references.bib"
csl: "ecology.csl"

You can download just about any journal’s style file here.

In-text

There are two options for citations in R Markdown documents, both based upon the standard Author Year format. BibTeX entries have a “citekey” that begins with @ by which they can be referenced. So, for example, if we had this reference in our .bib library

@Article{Smith_2021,
  year = {2021},
  publisher = {The Ecological Society of America},
  volume = {123},
  number = {2},
  pages = {1-10},
  author = {Sarah Smith and Joe Johnson},
  title = {Probably the best paper ever written},
  journal = {Ecology},
}

we could use [@Smith_2021] to format the in-text reference as “(Smith and Johnson 2021)”, or we could use @Smith_2021 to format the in-text reference as “Smith and Johnson (2021)”.